1. Hi Mark: As your suggestion, I reinstalled GMX4.6.1, when I run CMAKE using
*$**cmake ../ \* *-DCMAKE_INSTALL_PREFIX=/public/software/gromacs-4.6_avx \* *-DGMX_MPI=ON \* *-DCMAKE_C_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicc \* * -DCMAKE_CXX_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicxx \* * -DGMX_BINARY_SUFFIX=_mpi \* *-DGMX_CPU_ACCELERATION=AVX_256\* *-DFFTWF_INCLUDE_DIR=/public/software/mathlib/fftw332-float/include \* ***-DFFTWF_LIBRARY=/public/software/mathlib/fftw332-float/lib/libfftw3f.so* I met an error: ----------------------------------------------------- -- Performing Test _finite_compile_ok -- Performing Test _finite_compile_ok - Failed -- Checking for _finite - no -- Checking for system XDR support -- Checking for system XDR support - present CMake Error at CMakeLists.txt:880 (MESSAGE): Unrecognized option for accelerated kernels: AVX_256-DFFTWF_INCLUDE_DIR=/PUBLIC/SOFTWARE/MATHLIB/FFTW332-FLOAT/INCLUDE. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX -- Configuring incomplete, errors occurred! ----------------------------------------------------- Could you give me some advise? Thank you very much! Best, Yukun 2013/4/12 Mark Abraham <mark.j.abra...@gmail.com> > On Thu, Apr 11, 2013 at 5:41 PM, Yorquant Wang <wangy...@gmail.com> wrote: > > > Hello: > > I have installed GMX4.6.1 and GMX4.5.5 on the same cluster. There > are > > 2 Xoen E5 2630CPU in one node on this cluster. I tested the performance > of > > those two versions of GMX, found GMX4.6.1 only had 0.62 performance of > > GMX4.5.5. > > When I checked the .log file of GMX4.6.1, I found > > ... > > CPU acceleration: NONE > > FFT library: FFTW 3.2 wrappers to MKL > > Large file support: enabled > > RDTSCP usage: disabled > > Built on: Mon Apr 8 10:46:58 CST 2013 > > Built by: root@node3 [CMAKE] > > Build OS/arch: Linux 2.6.18-274.el5 x86_64 > > Build CPU vendor: Unknown, detect failed > > Build CPU brand: Unknown, detect failed > > > > Whatever your build system is was too weird/new for the auto-detection > system to cope with. And perhaps the assumption that your build CPU and > your mdrun CPU are the same is not valid. > > > > Build CPU family: 0 Model: 0 Stepping: 0 > > Build CPU features: > > C compiler: /public/software/mpi/openmpi-16-intel/bin/mpicc Intel > > icc (ICC) 12.1.0 20111011 > > C compiler flags: -std=gnu99 -Wall -ip -funroll-all-loops -O3 > > -DNDEBUG > > > > So I think my installed GMX4.6.1 failed to use AVX_256 kenerl. The > > installed commend is below. Could someone give some suggestion how to > solve > > this problem? Thank you very much! > > > > Since the detection is failing for unknown reasons, you will need to select > an appropriate acceleration for your mdrun *execution* environment in your > call to CMake, e.g. with -DGMX_CPU_ACCELERATION=AVX_256. > > Mark > > > > *$cmake ../ \* > > > > *-DCMAKE_INSTALL_PREFIX=/public/software/gromacs-4.6 \* > > > > *-DGMX_MPI=ON \* > > > > *-DCMAKE_C_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicc \* > > > > *-DCMAKE_CXX_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicxx \* > > > > * -DGMX_BINARY_SUFFIX=_mpi \* > > > > *-DFFTWF_INCLUDE_DIR=/public/software/mathlib/fftw331-float/include \* > > > > *-DFFTWF_LIBRARY=/public/software/mathlib/fftw331-float/lib/libfftw3f.so > * > > > > *$make –j 6* > > > > *$make install* > > > > Cheers up > > -- > > Yukun Wang > > PhD candidate > > Institute of Natural Sciences && College of Life Science, Shanghai Jiao > > Tong University > > Cell phone: 13621806236. > > China Shanghai > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Yukun Wang PhD candidate Institute of Natural Sciences && College of Life Science, Shanghai Jiao Tong University Cell phone: 13621806236. China Shanghai -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists